Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison	
1	Measured	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Subtracted	41482.5	33356.5	8126	
1	Measured	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	450.5	2394.5	5.31521	
1	Ranked	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	215	322	107	
1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	10	24	2.4	
1	Squared	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	468498	322755	145743	
1	Squared	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	48.0356	1357.07	28.2513	
1	Rooted	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	21.225	48.9336	2.30547	
1	Rooted	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	21.225	48.9336	27.7086	
2	Measured	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	41482.5	33356.5	8126	
2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	450.5	2394.5	5.31521	
2	Ranked	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	215	322	107	
2	Ranked	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Divided	15	28	1.86667	
2	Squared	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Subtracted	407289	263351	143938	
2	Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	48.0356	1357.07	28.2513	
2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	21.225	48.9336	2.30547	
2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	21.225	48.9336	27.7086	
3	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	41482.5	33356.5	8126	
3	Measured	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	2597.5	698.5	3.71868	
3	Ranked	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Divided	15	28	1.86667	
3	Ranked	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	337	232	105	
3	Squared	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	407289	263351	143938	
3	Squared	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	1596.92	115.48	13.8285	
3	Rooted	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	50.9657	26.4292	1.92839	
3	Rooted	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	50.9657	26.4292	24.5365	
4	Measured	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	41482.5	33356.5	8126	
4	Measured	hbs1-like. [source:refseq;acc:nm_006620]	Divided	2597.5	698.5	3.71868	
4	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Divided	15	28	1.86667	
4	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	337	232	105	
4	Squared	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	407289	263351	143938	
4	Squared	hbs1-like. [source:refseq;acc:nm_006620]	Divided	1596.92	115.48	13.8285	
4	Rooted	hbs1-like. [source:refseq;acc:nm_006620]	Divided	50.9657	26.4292	1.92839	
4	Rooted	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	50.9657	26.4292	24.5365	
5	Measured	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	41482.5	33356.5	8126	
5	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	1153.5	339.5	3.39764	
5	Ranked	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	15	28	1.86667	
5	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	212	309	97	
5	Squared	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	407289	263351	143938	
5	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	314.926	27.2805	11.544	
5	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	145.551	168.796	23.245	
5	Rooted	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	33.9632	18.4255	1.84327	
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	1153.5	339.5	3.39764	
6	Measured	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	44490.5	36927.5	7563	
6	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Divided	15	28	1.86667	
6	Ranked	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	212	309	97	
6	Squared	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	407289	263351	143938	
6	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	314.926	27.2805	11.544	
6	Rooted	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	33.9632	18.4255	1.84327	
6	Rooted	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Subtracted	145.551	168.796	23.245	
7	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	21185	28492	7307	
7	Measured	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Divided	1153.5	339.5	3.39764	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/